Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Segmentation
by Alana Shepherd 09 Feb '12

09 Feb '12

Hi Freesurfers, I've been using version 5.1 and looking at the desikan parcellation. I've been finding in quite a number of participants that the insula is extending medially towards the accumbens region (example screen shot attached), and wondered whether this is something I need to be manually editing. What would you advise? Kind regards, Alana Shepherd

1 0

How do I compile a table from several hundred "wmparc.stats" files?
by Tracy Abildskov 09 Feb '12

09 Feb '12

Hello surfers: I was wondering if there is a command like "aparcstats2table" or "asegstats2table" that would work with data in the "wmparc.stats" files. If I needed to compile the data on just a few scans I would not post this question. The problem is I need to compile this list on several hundred analyzed scans. Thank you, in advance, for any help you can offer. BA P.S. I know that wmparc.stats is not as good as aseg.ststs however it is the only place I can find some of this types of data.

3 2

wm_excluded
by Gabor Perlaki 09 Feb '12

09 Feb '12

Dear all, I'm new in freesurfer. I ran "recon-all -all" on 8 subjects without error, and I loaded the wm.mgz and the surfs. White matter surface (yellow line) seems pretty good by visual inspection, but the wm.mgz seems not so good everywhere. There are certain white-matter areas, which are clearly inside the yellow line (WM surface) but they are not considered as white-matter on the wm.mgz image. So it seems for me that calculating white-matter volume is more accurate using the white-matter surface instead of wm.mgz. What does wm.mgz used for? Does it has any impact on the white-matter volume reported by freesurfer? Is it a problem, that wm.mgz doesn't fit well the white-matter surface everywhere? What is the reason that wm.mgz doesn't fit the WM surface everywhere? Thanks a lot, Gabor

2 1

selxavg3-sess error
by Daniel Cole 09 Feb '12

09 Feb '12

Hello Freesurfers, I'm running into problems using fs-fast for a polar only, retinotopic analysis. The error message I get after running " " is: > Retinotopy dcole$ selxavg3-sess -analysis rtopy.self.lh -sf sessid > > Surface data self lh > > -------------------------------------------------------------- > > selxavg3-sess logfile is >> /rcbiUsers/dcole/Retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120209144554.log > > -------------------------------------------------------------- > > preproc-sess -s VGP01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh >> -nolog > > -------------------------------------------------------------- > > preproc-sess logfile is /dev/null > > -------------------------------------------------------------- > > $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ > > dcole > > setenv FREESURFER_HOME /Volumes/RCBI/freesurfer > > setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test > > Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 >> 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64 > > /rcbiUsers/dcole/Retinotopy > > /Volumes/RCBI/freesurfer/fsfast/bin/preproc-sess > > -s VGP01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog > > Thu Feb 9 14:45:54 EST 2012 > > instem f > > mc 1 f fmcpr > > stc 0 fmcpr > > sm 0 > > mask 1 brain > > VGP01 Template ----------------------------- > > mktemplate-sess -s VGP01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -nolog >> -update > > > > Session: /rcbiUsers/dcole/Retinotopy/VGP01 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > Detected input format at nii > > VGP01 Update not needed > > Run: 001 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > VGP01 001 Update not needed > > Run: 002 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > VGP01 002 Update not needed > > Run: 003 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > VGP01 003 Update not needed > > Run: 004 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > VGP01 004 Update not needed > > Run: 005 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > VGP01 005 Update not needed > > Thu Feb 9 14:45:55 EST 2012 > > mktemplate-sess completed > > VGP01 Mask ------------------------ > > mkbrainmask-sess -maskstem brain -fsd bold -s VGP01 -d >> /rcbiUsers/dcole/Retinotopy -nolog -update > > ------------------------------------------------ > > /rcbiUsers/dcole/Retinotopy/VGP01 > > Thu Feb 9 14:45:55 EST 2012 > > VGP01 Update not needed for session-level mask > > VGP01 Update not needed for run 001 mask > > VGP01 Update not needed for run 001 meanval > > VGP01 Update not needed for run 002 mask > > VGP01 Update not needed for run 002 meanval > > VGP01 Update not needed for run 003 mask > > VGP01 Update not needed for run 003 meanval > > VGP01 Update not needed for run 004 mask > > VGP01 Update not needed for run 004 meanval > > VGP01 Update not needed for run 005 mask > > VGP01 Update not needed for run 005 meanval > > Thu Feb 9 14:45:55 EST 2012 > > mkbrainmask-sess done > > VGP01 Registration ----------------------------- > > register-sess -s VGP01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 >> -per-run -nolog -update > > -------------------------------------------------------------- > > register-sess logfile is /dev/null > > -------------------------------------------------------------- > > Thu Feb 9 14:45:55 EST 2012 > > >> setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test > > cd /rcbiUsers/dcole/Retinotopy > > /Volumes/RCBI/freesurfer/fsfast/bin/register-sess -s VGP01 -d >> /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update > > >> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 >> 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64 > > > > Session: /rcbiUsers/dcole/Retinotopy/VGP01 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Run: 001 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 002 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 003 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 004 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 005 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Thu Feb 9 14:45:55 EST 2012 > > register-sess completed > > VGP01 MC ----------------------------- > > mc-sess -fstem f -fmcstem fmcpr -s VGP01 -d /rcbiUsers/dcole/Retinotopy >> -fsd bold -per-run -nolog -update > > Logfile is /dev/null > > ------------------------------------------- > > /rcbiUsers/dcole/Retinotopy/VGP01 > > RunList: 001 002 003 004 005 > > VGP01 001 Update not needed > > VGP01 002 Update not needed > > VGP01 003 Update not needed > > VGP01 004 Update not needed > > VGP01 005 Update not needed > > >> >> Thu Feb 9 14:45:55 EST 2012 > > mc-sess completed SUCCESSFULLY > > VGP01 To Surface ----------------------------- > > rawfunc2surf-sess -fwhm 5 -s VGP01 -d /rcbiUsers/dcole/Retinotopy -fsd >> bold -hemi lh -self -nolog -update > > instem fmcpr > > outstem fmcpr.sm5.self.hemi > > ------------------------------ > > 1/1 VGP01 > > 1/1 VGP01 001 lh --------- > > Thu Feb 9 14:45:55 EST 2012 > > VGP01 001 Update not needed > > 1/1 VGP01 002 lh --------- > > Thu Feb 9 14:45:55 EST 2012 > > VGP01 002 Update not needed > > 1/1 VGP01 003 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > VGP01 003 Update not needed > > 1/1 VGP01 004 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > VGP01 004 Update not needed > > 1/1 VGP01 005 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > VGP01 005 Update not needed > > >> Thu Feb 9 14:45:56 EST 2012 > > rawfunc2surf-sess completed > > ---------------------------------------- > > Started at Thu Feb 9 14:45:54 EST 2012 > > Ended at Thu Feb 9 14:45:56 EST 2012 > > preproc-sess done > > ------------------------------------------- > > /rcbiUsers/dcole/Retinotopy/VGP01 > > Thu Feb 9 14:45:56 EST 2012 > > anadir = /rcbiUsers/dcole/Retinotopy/VGP01/bold/rtopy.self.lh > > DoGLMFit = 1 > > DoContrasts = 1 > > UpdateNeeded = 1 > > ------------------------------------------ > > ------- matlab output -------------------- > > Warning: Unable to open display 'iconic'. You will not be able to display >> graphics on the screen. > > 2012-02-09 14:45:56.773 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.775 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.776 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.777 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.778 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.779 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.780 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.781 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.783 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.796 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.797 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.798 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.812 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.813 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:56.815 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > >> < M A T L A B (R) > > > Copyright 1984-2010 The MathWorks, Inc. > > Version 7.10.0.499 (R2010a) 64-bit (maci64) > > February 5, 2010 > > >> 2012-02-09 14:45:57.634 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.637 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.638 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.640 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.641 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.642 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.644 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.645 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.647 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.648 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.650 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.652 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.653 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.655 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.656 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.658 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.659 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.661 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.662 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.664 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.665 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.667 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.668 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > 2012-02-09 14:45:57.670 MATLAB[17738:7103] This process is attempting to >> exclude an item from Time Machine by path without administrator privileges. >> This is not supported. > > > > To get started, type one of these: helpwin, helpdesk, or demo. > > For product information, visit www.mathworks.com. > > > > >> >> >> >> >> >> >> >> /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > >> #@# VGP01 ############################### > > /rcbiUsers/dcole/Retinotopy/VGP01 > > ------------------------- > > $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ > > /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m > > /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > /Volumes/RCBI/freesurfer/matlab/MRIread.m > > ------------------------- > > outtop = /rcbiUsers/dcole/Retinotopy > > Extension format = nii.gz > > nruns = 5 > > autostimdur = > > >> >> outanadir = /rcbiUsers/dcole/Retinotopy/VGP01/bold/rtopy.self.lh > > Found 15746/149363 (10.5) voxels in mask > > Creating Design Matrix > > ... creation time = 0.011 sec > > DoMCFit = 1 > > ntptot = 1305, nX = 39, DOF = 1266 > > Saving X matrix to >> /rcbiUsers/dcole/Retinotopy/VGP01/bold/rtopy.self.lh/Xtmp.mat > > ??? Error using ==> svd > > Input to SVD must not contain NaN or Inf. > > >> Error in ==> cond at 40 > > s = svd(A); > > >> Error in ==> fast_selxavg3 at 254 > > XCond = cond(XtX); > > > > >> ------------------------------------------ > > ERROR: fast_selxavg3() failed\n > > I think the problem is with the "??? Error using ==> svd... " error, not the matlab errors. I've found that many people were reporting this matlab error but it's presumably more of an annoyance than a technical issue. I'm following the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . I'm pretty sure I have my directories set up properly and I've used Mricron's dcm2nii tool on my raw functionals/structurals. I've also already successfully preprocessed my data and made the rtopy.par files (preproc-sess & mkanalysis-sess). I haven't been able to find a response that fixed the problem and was hoping for some suggestions. Thanks so much, Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10(a)u.rochester.edu

1 0

Pial and white surface defects.
by Rashmi Singh 09 Feb '12

09 Feb '12

Hello, I had this issue raised earlier, but may be it got lost in the pile of questions you receive everyday. I am very new to freeSurfer, and may be its me who is dong something wrong so please advise. I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and I noticed (volume data view using tkmedit) that in most of my subjects the freesurfer has included non-cortical matter (ex: cerebellar regions) as cortical matter and have excluded several white matter voxels. I use brainmask volume loaded as main volume and white matter volume loaded as aux volume to inspect the final pial and white surfaces. These defects are more clearly visible when I get the subcortical segmentation in on mode to be viewed or when I am viewing the pial/white surface boundaries in the images where brainmask is loaded as main volume with T1.mgz as the aux volume and subcortical segmantation in on mode. Interestingly such defects were found in same regions across the subject and are present in more than one section. If what I am seeing are defects, this would be require too much editing. Please advise Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

Error - Need help
by Darshan Suryanarayan Pai 08 Feb '12

08 Feb '12

I have CentOS 5 installed through VMware player on a WIn 7 desktop . I had freesurfer installed on it and I was running a subject . This subject ran through completely on freesurfer installed on MacOSx. However on the virtual Linux setup it failed with the following error Loading Source Label Invalid Argument Error reading from <Data Folder>/fsaverage/label/lh.BA1.label. I checked and did not find this folder in the system. I was hoping if someone here has any idea of what went wrong Regards Darshan

2 2

setting a cluster size and thresholding in tksurfer
by Ritobrato Datta 08 Feb '12

08 Feb '12

Hi I am displaying the fMRI results in tksurfer. Is there a way in tksurfer to set a cluster size (for eg 50 vertices) and display only those activated regions which have bigger clusters than 50 ? Thanks Ri

1 0

FreeSurfer Lab seeks Research Assistant
by Allison Player 08 Feb '12

08 Feb '12

Please forward to anyone you think may be interested: Position involves working in a fast-paced Computational Neuroimaging Lab. The lab develops and maintains software for MR image analysis and works primarily in a UNIX environment. The lab is also responsible for several in vivo and ex vivo (human) MRI projects. We are seeking a Research Assistant to take on several job responsibilities from a list of potential responsibilities. The Research Assistant would be responsible for work on several projects. One major project would be assisting with the scanning for the Vietnam Era Twin Study of Aging (VETSA), a large-scale research project on cognitive aging in twins. Scans are early Wednesday and Saturday mornings, every week, March through August and every other week (or less) for the rest of the year. In addition to the above, the Research Assistant would help with high resolution ex vivo scanning projects on the 3 and 7 Tesla MRI scanners. Candidate must be willing to work evenings and weekends to perform some of the experiments, including being on call during designated weekends to respond to technical problems. Candidate must also be comfortable interacting with brain tissue. Other potential projects may include: -Quality checking in vivo MRI data that has been processed by the FreeSurfer software package and manually fixing errors. -Debugging and testing specific elements of FreeSurfer. For this and the above project, the candidate must be comfortable with computers and beta testing software. -Assisting with histological processing: sectioning, mounting, histochemical and immunocytochemical staining. -Manually labeling in vivo and ex vivo MRI images. Candidate should be able to work independently, show initiative, be confident in making decisions, able to multitask, not easily stressed, and one who is not easily discouraged by failed experiments but enjoys a challenge. Candidate should have a Bachelor's or Master's Degree. Relevant backgrounds would be Neuroscience, Psychology, Engineering, Computer Science, and/or Biology. A responsible individual with a flexible schedule is required. Experience in imaging and knowledge of UNIX and scripting is preferred. Knowledge of neuroanatomy or programming is a plus. Position offers great opportunities to work with prominent scientists, people from a variety of fields, a famous Research Center, a great and fun team, opportunities to publish, as well as guidance and support for future career choices. Please send resumes and cover letters to Allison Stevens at this email address.

1 0

mri_compile_edits
by Michael Harms 08 Feb '12

08 Feb '12

Hi Nick, Why does mri_compile_edits (-showedits flag) report edits to brainmask.mgz (both in the edits.mgz volume and its text output) if no manual edits were actually performed -- i.e, if brainmask.mgz and brainmask.auto.mgz are identical? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 1

Defects in freesurfer output
by Rashmi Singh 08 Feb '12

08 Feb '12

Hello, I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and I noticed (volume data view using tkmedit) that in most of my subjects the freesurfer has included non-cortical matter (ex: cerebellar regions) as cortical matter and have excluded several white matter voxels. I use brainmask volume loaded as main volume and white matter volume loaded as aux volume to inspect the final pial and white surfaces. These defects are more clearly visible when I get the subcortical segmentation in on mode to be viewed or when I am viewing the pial/white surface boundaries in the images where brainmask is loaded as main volume with T1.mgz as the aux volume and subcortical segmantation in on mode. Interestingly such defects were found in same regions across the subject and are present in more than one section. If what I am seeing are defects, this would be require too much editing. I am very new to freeSurfer, please advise. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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